rs56167332

Variant names:

• chr5-159400761-C-A
• rs56167332
• ENST00000635333.1:n.327+8184C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-159400761-C-A
• chr5-159400761-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635333.1(ENSG00000249738):​n.327+8184C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,088 control chromosomes in the GnomAD database, including 6,700 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6700 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 26 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000635333.1	n.327+8184C>A		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-15763C>A		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-15763C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44156 AN: 151970 Hom.: 6694 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.303

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44178 AN: 152088 Hom.: 6700 Cov.: 32 AF XY: 0.289 AC XY: 21503 AN XY: 74352

African (AFR) AF: 0.192 AC: 7982 AN: 41512

American (AMR) AF: 0.275 AC: 4206 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5172

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4816

European-Finnish (FIN) AF: 0.296 AC: 3126 AN: 10552

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23302 AN: 67962

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.239 Hom.: 1781

Bravo AF: 0.284

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.2
DANN	Benign	0.80
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56167332; hg19: chr5-158827769;